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Yorodumi- PDB-5ho0: Crystal structure of AbnA (closed conformation), a GH43 extracell... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5ho0 | ||||||
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Title | Crystal structure of AbnA (closed conformation), a GH43 extracellular arabinanase from Geobacillus stearothermophilus | ||||||
Components | Extracellular arabinanase | ||||||
Keywords | HYDROLASE / GH43 / arabinanase / Geobacillus stearothermophilus / extracellular | ||||||
Function / homology | Function and homology information hydrolase activity, hydrolyzing O-glycosyl compounds / carbohydrate metabolic process / metal ion binding Similarity search - Function | ||||||
Biological species | Geobacillus stearothermophilus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.35 Å | ||||||
Authors | Lansky, S. / Shwartstien, S. / Salama, R. / Shoham, Y. / Shoham, G. | ||||||
Citation | Journal: To Be Published Title: Crystal structure of AbnA (closed conformation), a GH43 extracellular arabinanase from Geobacillus stearothermophilus Authors: Lansky, S. / Shwartstien, S. / Salama, R. / Shoham, Y. / Shoham, G. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5ho0.cif.gz | 183 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5ho0.ent.gz | 141.1 KB | Display | PDB format |
PDBx/mmJSON format | 5ho0.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ho/5ho0 ftp://data.pdbj.org/pub/pdb/validation_reports/ho/5ho0 | HTTPS FTP |
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-Related structure data
Related structure data | 2x8tS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 94131.516 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Geobacillus stearothermophilus (bacteria) Gene: abnA / Production host: Escherichia coli (E. coli) / References: UniProt: B3EYN2 |
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-Non-polymers , 5 types, 432 molecules
#2: Chemical | #3: Chemical | ChemComp-TRS / | #4: Chemical | ChemComp-EDO / | #5: Chemical | ChemComp-EPE / | #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.13 Å3/Da / Density % sol: 42.26 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 17%-19% PEG 6K, 0.2M NaCl, 0.1M HEPES buffer, pH 7 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.976 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Dec 10, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.976 Å / Relative weight: 1 |
Reflection | Resolution: 2.35→50 Å / Num. obs: 33468 / % possible obs: 98 % / Redundancy: 6 % / Rmerge(I) obs: 0.104 / Net I/σ(I): 8.4 |
Reflection shell | Resolution: 2.35→2.39 Å / Redundancy: 4.5 % / Rmerge(I) obs: 0.56 / Mean I/σ(I) obs: 2.2 / % possible all: 86 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2X8T Resolution: 2.35→42.25 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.907 / SU B: 8.578 / SU ML: 0.201 / Cross valid method: THROUGHOUT / ESU R: 0.515 / ESU R Free: 0.283 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 36.627 Å2
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Refinement step | Cycle: 1 / Resolution: 2.35→42.25 Å
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Refine LS restraints |
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